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Old 01-18-2013, 07:15 AM   #5
cpleis
Junior Member
 
Location: Urbana, IL

Join Date: Oct 2012
Posts: 8
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Hi SHeaph,
Unfortunately I was not able to resolve the issue. I think that the heat map function in R isn't able to resolved such a large number of data labels. I simply switched to showing the functional groups instead of individual genes and the heat map turned out fine. I've attached the final image I created and the code I used to create it (below).

**Using logFC data for only sig genes (FDR < 0.05)

install.packages("gplots")
library(gplots)
source("http://bioconductor.org/biocLite.R")
biocLite("ALL")

heatdata <- read.csv("Avg_log2FC_allbins_sig.csv", sep=",")
heatdata <- heatdata[,2:5]
heatdata_matrix <- data.matrix(heatdata)
pdf("Heatmap_all.pdf", width=10, height=5, paper="a4r")
data_heatmap <- heatmap.2(heatdata_matrix, col=redblue(75), scale="row",
key=TRUE, symkey=FALSE, density.info="none", trace="none", margins=c(10,10), labRow =rownames(heatdata_matrix),cexRow=0.5)
axis(4,
at=2:NROW(heatdata_matrix),
labels=rownames(heatdata_matrix[data_heatmap$rowInd] ),
cex=0.5)
dev.off()

If you do find another solution let me know!

Courtney
Attached Files
File Type: pdf Heatmap_all.pdf (7.3 KB, 327 views)
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